############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:scBubbletree.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings scBubbletree_1.7.7.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/scBubbletree.Rcheck’ * using R version 4.4.0 Patched (2024-04-24 r86482) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.4 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘scBubbletree/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘scBubbletree’ version ‘1.7.7’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘scBubbletree’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE compare_bubbletrees: no visible binding for global variable ‘JD’ compare_bubbletrees: no visible binding for global variable ‘intersection’ get_bubbletree_dummy: no visible global function definition for ‘as.dist’ get_bubbletree_dummy: no visible global function definition for ‘hclust’ get_bubbletree_graph: no visible global function definition for ‘as.dist’ get_bubbletree_graph: no visible global function definition for ‘hclust’ get_bubbletree_kmeans: no visible global function definition for ‘kmeans’ get_bubbletree_kmeans: no visible global function definition for ‘as.dist’ get_bubbletree_kmeans: no visible global function definition for ‘hclust’ get_gap_k : get_Wk: no visible global function definition for ‘kmeans’ get_gap_k : : no visible global function definition for ‘runif’ get_gap_k: no visible binding for global variable ‘var’ get_gap_r : : no visible global function definition for ‘runif’ get_gap_r: no visible binding for global variable ‘var’ get_gap_r_k1 : : no visible global function definition for ‘runif’ get_gap_r_k1: no visible binding for global variable ‘var’ get_k: no visible binding for global variable ‘kmeans’ get_k: no visible binding for global variable ‘var’ get_r: no visible binding for global variable ‘var’ Undefined global functions or variables: JD as.dist hclust intersection kmeans runif var Consider adding importFrom("stats", "as.dist", "hclust", "kmeans", "runif", "var") to your NAMESPACE file. * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed get_r 11.014 0.199 12.179 get_gini_k 8.940 0.193 10.320 get_bubbletree_dummy 8.725 0.119 9.832 get_num_violins 6.068 0.090 6.838 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: [ FAIL 4 | WARN 1 | SKIP 0 | PASS 477 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-input-get-num-tiles.R:341:3'): btd argument ────────────────── `get_bubbletree_graph(...)` did not produce any warnings. ── Failure ('test-input-get-num-tiles.R:397:3'): btd argument ────────────────── `get_num_tiles(...)` did not throw an error. ── Failure ('test-input-get-num-violins.R:159:3'): btd argument ──────────────── `get_bubbletree_graph(...)` did not produce any warnings. ── Failure ('test-input-get-num-violins.R:192:3'): btd argument ──────────────── `get_num_violins(...)` did not throw an error. [ FAIL 4 | WARN 1 | SKIP 0 | PASS 477 ] Error: Test failures Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 1 NOTE See ‘/Users/biocbuild/bbs-3.20-bioc/meat/scBubbletree.Rcheck/00check.log’ for details.